Not really the case; you're misunderstanding the term second system effect.

    > The general tendency is to over-design the second system, using all the ideas and frills that were cautiously sidetracked on the first one.  The result, as Ovid says is a "big pile".  For example, consider the IBM 709 architecture, later embodied in the 7090.  This is an upgrade, a second system for the very successful and clean 704.  The operation set is so rich and profuse that only about half of it was regularly used.  (p.55)
    > 
    > The second-system effect has another manifestation somewhat different from pure functional embellishment.  That is a tendency to refine techniques whose very existence has been made obsolete by changes in basic system assumptions. (p.56)  

It's the exact opposite: by explicitly dictating what is correct, perfect, and standard in this codebase, we achieve very high consistency and quality with very little "embellishment" and excess because the LLM is following a set of highly curated instructions rather than the whims of each developer on the team.

Suggest that you re-read what Brooks meant by "second system effect".